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Ant-termite interactions in New Guinea coconut plantations.
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StratigrapheR: making and using lithologs in R
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StratigrapheR is an open-source integrated stratigraphy package. It is available in the free software environment R (https://CRAN.R-project.org/package=StratigrapheR) and is designed to generate lithologs in a semi-automated way, to process stratigraphical information, and to visualize any plot along the lithologs in the R environment. The basic graphical principle behind StratigrapheR is the incremental addition of elements to a drawing: a plot is opened, and graphical elements are successively added. This allows compartmentalisation of the drawing process, as well as the superposition of different plots for comparison. For instance a litholog of a single section can be written as a single function including all the drawing sub-functions, and be integrated in a larger plot, for instance to be correlated to other sections or to show proxy data. The StratigrapheR package is designed for efficient work, and minimum coding, while still allowing versatility. The lithological information of beds (upper and lower boundary, hardness, lithology, etc.) is converted into polygons. All polygons are drawn together using a single function, and each polygon can have its personalised symbology allowing to distinguish lithologies. A similar workflow can be used for plotting proxies while distinguishing each sample by their lithology. Vector graphics can be imported as SVG files, and precisely drawn with the lithologs to serve as symbols or complex elements. Every type of symbol is plotted by calling one single function which repeats the drawing for each occurrence of the represented feature. This illustrates that the amount of work invested to make lithologs using StratigrapheR is related to their complexity rather than their length: a long but monotonous litholog (e.g. of marl-limestone alternations) only takes a few lines of code to generate. The StratigrapheR package also provides a set of functions to deal with selected stratigraphic intervals (for instance in the [0,1[ form): they allow simplification, merging, inversion and visualisation of intervals, as well as identifying the samples included in the given intervals, and characterising the relation of the intervals with each other (overlap, neighbouring, etc.). StratigrapheR includes PDF and SVG generation of plots, of any dimension. The generated PDF can even store multiple plots in a single file (each plot on a different page) to document data processing comprehensively.
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RBINS Staff Publications 2020
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A posteriori verification methodology for astrochronology: a step further to improve the falsifiability of cyclostratigraphy
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Cyclostratigraphy is increasingly used to improve the Geologic Time Scale and our understanding of past climatic systems. However, except in a few existing methodologies, the quality of the results is often not evaluated. We propose a new methodology to document this quality, through a decomposition of a signal into a set of narrow band components from which instantaneous frequency and amplitude can be computed, using the Hilbert transform. The components can be obtained by Empirical Mode Decomposition (EMD), but also by filtering a signal (be it tuned or not) in any relevant way, and by subsequently performing EMD on the signal minus its filtered parts. From that decomposition, verification is performed to estimate the pertinence of the results, based on different concepts that we introduce: Integrity quantifies to what extent the sum of the components is equal to the signal. It is defined as the cumulated difference between (1) the signal, and (2) the summed components of the decomposition. EMD fulfils integrity by design, except for errors caused by floating-decimal arithmetic. Ensemble Empirical Mode Decomposition (EEMD) may fail to satisfy integrity unless noisy realisations are carefully chosen in the algorithm to cancel each other when averaging the realisations. We present such an algorithm implemented in R: “extricate”, which performs EEMD in a few seconds. Parsimony checks that the decomposition does not generate components that heavily cancel out. We propose to quantify it as the ratio between (1) the cumulated absolute values of each component (except the trend), and (2) the cumulated absolute values of the signal (minus the trend). The trend should be ignored in the calculation, because an added trend decreases the parsimony estimation of a similar decomposition. IMF departure (IMFD) quantifies the departure of each component to the definition of intrinsic mode functions (IMF), from which instantaneous frequency can reliably be computed. We define it as the mean of the absolute differences of the base 2 logarithms of frequencies obtained using (1) a robust generalized zero-crossing method (GZC, which simplifies the components into extrema separated by zero-crossings) and (2) a more local method such as the Hilbert Transform. Reversibility is the concept that all initial data points are preserved, even after linear interpolation and tuning. This allows to revert back to the original signal and discuss the significance of each data point. To facilitate reversibility we introduce the concept of quanta (smallest depth or time interval having significance for a given sampling) and an algorithm computing the highest rational common divisor of given values in R: “divisor”. This new methodology allows to check the final result of cyclostratigraphic analysis independently of how it was performed (i.e. a posteriori). Once the above-mentioned concepts are taken into account, the instantaneous frequencies, ratios of frequencies and amplitudes of the components can be computed and used to interpret the pertinence of the analysis in a geologically meaningful way. The instantaneity and independence of frequency and amplitude so obtained open a new way of performing time-series analysis.
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RBINS Staff Publications 2020
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Applying micro-CT imaging in the study of fossil sepiids and nautilids (Cephalopoda): examples from the Eocene of Belgium
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RBINS Staff Publications 2020
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NiphNet: a self-governing environmental monitoring network
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A high-precision and low-cost temperature and humidity logging device, called Niphargus and originally intended for environmental monitoring in caves, was developed at the Geological Survey of Belgium (Burlet et al., 2015). The Niphargus is designed as a standalone logger, with data to be retrieved manually whenever needed. This allows for a very small and simple electronic design, low power consumption and flexible placement. There are, however, a number of disadvantages for specific applications. For example, there is no feedback possible on malfunction or battery lifetime. To avoid loss of data during long-term measurement campaigns, regular inspection and data retrieval are necessary. Apart from the inconvenience, this manipulation also causes disturbance in the measurements. A new version of the Niphargus was therefore developed, including a wireless Digi XBee DigiMesh module. These modules communicate on a 868 MHz radio frequency, in a self-governing mesh network (Fig. 1). In such a network, every device is able to communicate to any other device within range. For data transmission, the most optimal pathway is chosen between transmitter and receiver. As such, in case of a single device malfunction, the connection between the other nodes can still be guaranteed. In case of the NiphNet, the receiving end includes a single-board computer with cellular network connectivity, from which data is uploaded to a cloud repository. From there, live monitoring data can be displayed online, downloaded and processed. A first successful test was conducted with a NiphNet of 5 devices in waterproof containers (Fig. 2) and online display at the GeoEnergy Test Bed in Nottingham, UK, in March 2018. Current and future efforts focus on the enclosure design and the automation of data readout over the network. There is a large array of possible applications. For environmental monitoring in caves, the individual nodes can ensure data transmission from a network of environmental sensors inside the cave to a station outside, allowing for continuous access to measurements and minimising the need for regular field inspection. This is currently being installed in the caves of Han. The geological storage of CO2 requires long-term monitoring to establish a baseline and detect leakage from the reservoir, both below and above ground. Such monitoring activities need to be maintained for several decades, and therefore need to be low effort and low cost. Near the surface, temperature is expected to be a good proxy for CO2 leakage when a network is set-up that can detect temperature anomalies in the range of 0.01°C. This is possible with a network of shallow buried Niphargus nodes. Then, wireless access to thesedevices is not only a matter of long-term and maintenance-free coverage of a large area. Detection of small temperature differences depends on not disturbing the shallow subsurface, and therefore on being able to download the data remotely.
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RBINS Staff Publications 2018
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Holocene Climate Variability in the Near East and its Impact on the History of Civilisation
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RBINS Staff Publications 2021
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Coastal coarse-clast deposits from storms vs. tsunamis
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RBINS Staff Publications 2021
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Klimadynamik und Küstenveränderungen – Einfluss auf die Kulturgeschichte Mesopotamiens
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RBINS Staff Publications 2021
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The Holocene palaeolake of Tayma – A key site for unravelling palaeoclimate, with implications for Neolithic incursions and “oasisation” on the northern Arabian Peninsula
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RBINS Staff Publications 2021
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Die holozäne Feuchtphase auf der Arabischen Halbinsel und Implikationen für die Entstehung der Oasenkultur
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RBINS Staff Publications 2021
